What options would I use to extract the 2 front channel flacs?
Haven't been on the last couple days. Sorry. Anyway, it sounds like you're using a GUI for eac3to. I don't, so I couldn't tell you what to do in one. But here's what you'd do at the command line in two easy steps:
Step 1: Let's analyze the file (you said it was an .mkv):
eac3to [filename].mkv
After the brief analysis, eac3to will output a list of the contents of the file. It will look something like this:
MKV, 1 video track, 1 audio track, 1 subtitle track, 0:25:29, 24p /1.001
1: h264/AVC, English, 1488x1080 24p /1.001
2: AC3, 5.1 channels, 640kbps, 48kHz
3: Subtitle (SRT), English
We can see the video is track 1, the audio is track 2, and the subtitles are track 3. I will use track 2 in my examples, but substitute whatever number is the audio track for your file.
Step 2: Now that we know what track to work with, let's decode the ac3 track and output it as individual .wav files per channel:
eac3to [filename].mkv 2: blah.wavs
With this command we're telling eac3to to work with track 2, decode and output the audio to multiple .wav files named blah (eac3to will add the channel to the name automatically). It will look something like this:
MKV, 1 video track, 1 audio track, 1 subtitle track, 0:25:29, 24p /1.001
1: h264/AVC, English, 1488x1080 24p /1.001
2: AC3, 5.1 channels, 640kbps, 48kHz
3: Subtitle (SRT), English
a02 Writing WAVs...
a02 Creating file "blah.C.wav"...
a02 Creating file "blah.L.wav"...
a02 Creating file "blah.R.wav"...
a02 Creating file "blah.SR.wav"...
a02 Creating file "blah.LFE.wav"...
a02 Creating file "blah.SL.wav"...
Video track 1 contains 36656 frames.
eac3to processing took 35 seconds.
Done.
And that's it, you're done. Now you can discard the channels you don't need (LFE, SR, SL) and do whatever you want with the L and R channels. Just in case this doesn't suit you and what you really want is a downmix of the 5.1 audio, use this command:
eac3to [filename].mkv 2: blah.flac -down2 -mixlfe
This will downmix the multichannel audio, including the LFE, to stereo and output a neat and tidy flac.
Hope this helps.